Transcript

2.
Credit
Icons from the Zotero interface are produced in this document. They were created by Mark
James and Yusuke Kamiyamane and published under CC BY license on the author's websites:
Mark James (http://www.famfamfam.com/)
Yusuke Kamiyamane (http://p.yusukekamiyamane.com/)
About this document
Course notes of the lecture given in EPFL's outpost in Fribourg on January 30, 2015.
You can download the PDF version from http://go.epfl.ch/zotero-course-notes.
Document version
v1.4 / january 2015
You have the right to reuse the content of this document but
derivative works should be published under CC BY-SA license. In
every case, you should credit this document with my name and the
name of the library. For further information about the license, see link
below.
Zotero: collecting, managing, sharing, citing references made easy by
Raphaël Grolimund (EPFL Library) is licensed under a Creative
Commons Attribution-ShareAlike 4.0 International License.
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3.
PROGRAM
Here is an overview of the course. This is more a thread than a real program.
Discover
Install
Collect Import
Setup
Manage Share
Create
More
Cite
First part of the course: Second part of the course:
Discover Create
Install Setup
Import Share
Collect Cite
Manage
The More section gathers some questions that go beyond the scope of this course, but that
could be useful.
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4.
DISCOVER
What is Zotero?
Zotero is a reference manager. It helps you collect bibliographic references, store and sort
them and manage a bibliography effortlessly.
And if you are writing a paper, Zotero makes citing very easy.
Zotero has first been developped as a Firefox add-on. Since January 2012, Zotero is also
provided as a standalone software with exactly the same interface, but with additional
compatibility with Chrome and Safari.
Zotero is developped since 2006 by the Center for History and New Media
(http://chnm.gmu.edu/) at George Mason University (http://www.gmu.edu/), Virginia (USA).
A brief history of Zotero
Oct. 2006 Zotero beta version
Oct. 2007 Zotero 1.0
Feb. 2010 Zotero 2.0 (sync and share features)
Mar. 2011 Zotero 2.1 (Firefox 4 compliant)
Jan. 2012 Zotero 3.0 (standalone version, Chrome & Safari compliant)
Apr. 2013 Zotero 4.0 (major improvements with new features)
Zotero is (and has always been) a free software. Free doesn't (only) mean it's free of charge, it
also means that no one owns Zotero.
First developped under ECL license1
, Zotero switched to GNU GPL v32
when the version 2.0
was released, before switching a second time to GNU AGPL3
(version 2.1.7).
You can expect from a reference manager to :
* add/import references automatically (or very easily)
* create a bibliography automatically (or very easily)
* help you cite while you write a paper
All these technical tasks should be done by the software. You save time for things the
software can't do for you:
* check if the reference data are correct and complete
* read papers
* sort references
* select relevant references to add in the bibliography
It is important to understand that this kind of software is made to manage references, not
items. It is not means for managing a private or a lab library (with functionalities for
borrowing documents).
Why Zotero ?
There are many reference managers. A comparison of reference managers is avaiblable on
Wikipedia4
.
1 http://opensource.org/licenses/ecl2.php (accessed Jan. 28, 2015)
2 http://www.gnu.org/licenses/gpl.html (accessed Jan. 28, 2015)
3 http://www.gnu.org/licenses/agpl.html (accessed Jan. 28, 2015)
4 http://en.wikipedia.org/wiki/Comparison_of_reference_management_software (accessed Jan. 28, 2015)
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6.
Zotero interface
The interface is divided in three parts. In the left part you see the collections and
subcollections (and groups) where you file your references. When you select a
(sub)collection, its content (the references) is displayed in the central part. And when you
click on a reference, all the metadata (title, author, ...) are displayed in the right part.
Personal notes
collection
& groups selected collection content
reference
metadata
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7.
Here are the interface buttons and their function.
New Collection... create a new collection (not a subcollection)
New Group... open Zotero website and create a new group
Actions access to import, export tools (among others) and preferences
New Item create a new empty reference
Create New item from Current Page save the current webpage (reference +
complete webpage snapshot)
Add Item by Identifier add reference by entering an ISBN, DOI or PMID9
New Note create a note linked to a reference or not
Add Attachment create an attachment (snapshot, file, picture, ...) to a reference
Advanced Search query on several fields at a time (with ability to save results)
Locate access to the document (not only the reference)
Sync with Zotero Server share the Zotero library across several devices
(computers, tablets, smartphones)
Toggle Tab Mode display Zotero in a browser tab (full screen)
Back to default display
9 ISBN, DOI and PMID are explained at the end of the Collect section.
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8.
INSTALL
What do you need to install (depending on your web browser and word processor).
1. What is your web browser?
Firefox install Zotero for Firefox (go to 2)
Chrome install Zotero Standalone
and install Zotero connector for Chrome (go to 3)
Safari install Zotero Standalone
and install Zotero connector pour Safari (go to 3)
IE, Opera ou autre Not yet compatible with Zotero10
2. What is the software you use to write your documents ?
Word install citation plugin for Word
OpenOffice.org/LibreOffice install citation plugin for OpenOffice.org/LibreOffice
LaTeX install Autozotbib11
3. You are done! The citation plugin is included in Zotero Standalone.
10 Bookmarklets for other browsers were released: works well with Opera (not with Internet Explorer). You can
download them on http://www.zotero.org/downloadbookmarklet (accessed Jan. 28, 2015).
11 For further information, see More section.
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9.
COLLECT
With Zotero, you collect references with a single click.
Zotero scans the webpage while it is loading in the web browser. If (at least) one
bibliographic reference is detected, Zotero displays an icon in the address bar (or just next to
it, if you use Safari). A single click on this icon adds the reference in your Zotero library.
Firefox
Chrome
Safari
Zotero can deal with a large number of document types (the most common are shown below).
Book Picture
Book Section Video Recording
Journal Article Encyclopedia Article
Conference Paper Blog Post
Thesis Web Page
Presentation Document (generic)
If Zotero detects more than one reference on a webpage, an yellow folder icon is displayed.
Clicking on this icon open a prompt where you can select the reference you want to add in
your Zotero library. They will all be added at the same time.
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10.
EXERCISE Add books from a library catalog or a bookstore you are used to visit.
Suggestions : http://library.epfl.ch/beast
http://www.amazon.com
Personal notes
EXERCISE Add some papers from databases you use on a regular basis.
Suggestions : http://www.webofknowledge.com (restricted access)
http://www.sciencedirect.com (restricted access)
http://scholar.google.com
Personal notes
EXERCISE Add a few thesis from Infoscience (EPFL Institutional Repository).
Suggestion : http://infoscience.epfl.ch
Personal notes
EXERCISE Add some presentations from a website you usually use for that.
Suggestion : http://www.slideshare.net
Personal notes
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11.
EXERCISE Add some pictures from a website you like to visit.
Suggestions : http://www.flickr.com
http://commons.wikimedia.org/
Personal notes
EXERCISE Add some videos.
Suggestions : http://www.youtube.com
http://www.vimeo.com
http://www.ted.com
Personal notes
EXERCISE Add a few encyclopedia entries.
Suggestions : http://en.wikipedia.org
Personal notes
QUESTION What can you do if a website is not Zotero-compliant?
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12.
For books and articles, a powerful option is provided: the Magic Wand.
ISBN, DOI and PMID
For books, Zotero sends a request to the Library of Congress catalog based on
the provided ISBN12
. If no result is found, the same request is sent to
WorldCat13
, the biggest library catalog in the world.
For journal papers, Zotero accepts DOI or PMID.
DOI (Digital Object Identifier14
) is a unique alphanumerical string assigned to
an online paper. It can be a journal paper, as well as a conference paper, a thesis
or any final online document. Zotero relies on CrossRef to find the document
matching with the DOI.
PMID (PubMed IDentifier) is a identifier assigned to papers in PubMed15
(bibliographical database containing biomedical literature). Indexed articles get
a PMID (no every article in PubMed gets one).
EXERCISE Use the identifier to add some papers and books provided in class.
Personal notes
12 ISBN stands for International Standard Book Number. It's a unique number assigned to every published
book.
13 As of January 2013, WorldCat gathers 2 billion item. Visit http://www.worldcat.org/ (accessed Jan. 28,
2015).
14 Further information on http://www.doi.org/ (accessed Jan. 28, 2015). ETH Zurich delivers DOI for
Switzerland. See http://www.doi.ethz.ch/index_e.html (accessed Jan. 28, 2015).
15 http://www.pubmed.com (accessed Jan. 28, 2015)
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13.
IMPORT
If already use a reference manager or store PDF on your computer, you can import them in
your Zotero library.
Import references
1. To export references from your former reference manager, choose the BibTeX or RIS file
format.
BibTeX and RIS
Both formats are standards and every reference manager should let your export
in at least one of those formats.
Warning ! Don't mix up exportation format and citation style. RIS and BibTeX
are exportation formats. They are used to be handled by computer, not by
humans16
. Here is what it looks like.
RIS Format
TY - BOOK
ID - 135
T1 - Zotero : a guide for librarians, researchers, and educators
CY - Chicago
A1 - Puckett,Jason
PB - Association of College and Research Libraries
PY - 2011///
KW - Zotero
SN - 9780838985892
ER -
BibTeX Format
@book{puckett_zotero_2011,
address = {Chicago},
title = {Zotero : a guide for librarians, researchers, and educators},
isbn = {9780838985892},
shorttitle = {Zotero},
publisher = {Association of College and Research Libraries},
author = {Puckett, Jason},
year = {2011},
keywords = {#bibliogr., #didac2011, #lu/vu, #obtenu}
}
16 Citation styles are discussed in the Cite section.
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14.
2. Import the file in Zotero (Actions > Import...).
Import PDF files (from the web)
When you download a PDF from the web using Firefox, a prompt asks if you want to save it
in Zotero. By default, Zotero will try to retrieve the metadata from the PDF.
If you use another web browser, you have to download the PDF on your computer first and
then drag and drop it in Zotero.
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15.
Import PDF files (from your computer)
1. Drag and drop PDF files in the central part of the Zotero interface.
2. Select them, right-click and choose
Retrieve Metadata from PDF in the dropdown
menu.
3. Zotero relies on Google Scholar to find
matches.
Note : Obviously, it won't work if the PDF file
has no metadata (typically an print article you
scanned).
4. If any, Zotero creates a reference and joins
the PDF as attachment.
(Optional)
5. The PDF file can be renamed based on the
title, author and date of the document.
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16.
EXERCISE Add some PDF files and try to retrieve the metadata as explained
above.
(If you have PDF files on your computer, try with these ones. If you don't, use the
one provided in class.)
Personal notes
EXERCISE Import the RIS file provided in class and organize the references in
your Zotero library.
Personal notes
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17.
SETUP
The Zotero Preferences panel allows you to setup many features. Let's have a look and see the
main points.
General Tab
Manages the way Zotero is displayed in the browser. You can also tell Zotero to open
downloaded RIS files and allow (or forbid) to automatically tag items with
keywords and subject headings.
Sync Tab > Settings
Sync references and files (together or not)
Search Tab
Install and update PDF Indexing tools (to retrieve references from PDF metadata).
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19.
MANAGE
Zotero provides several features to manage your library. Let's have a look at the main ones.
Organize
All the reference are included in My Library. Then, you can dispatch them in collections and
subcollections you create. You can add a reference in several (sub)collections.
If a (sub)collection is selected when you collect references, they will be automatically added
in it.
EXERCISE Organize the collected references in collections and subcollections.
Personal notes
Sort
You can choose how the references are sorted. It can be based on many field. To choose a
field, just click on the column header (click again to reverse the sort order).
EXERCISE Sort references based on the Date Added field (lastest first).
Personal notes
Tag
Managing and searching the Zotero library can be eased by adding tags to references.
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20.
You can assign a specific color up to 6 tags so that the tagged documents are easier to find in
your library. You can add these tags to your references by just pressing the related keystroke
(1-6).
By default, Zotero adds keywords and subjects headings provided on the platform where the
reference comes from. These tags are orange. The ones you add by yourself are blue. You can
choose not to get the keywords and subjects headings from the platform in the General Tab
of the Preferences panel.
EXERCISE Add some tags (for later use).
Personal notes
Search
Zotero provides two search mode.
The search field launches a quick search.
EXERCISE Run a quick search and see what happens.
Personal notes
The Advanced Search button (magnifying glass) offers more tools to build a query.
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21.
You can save a advanced search so that you don't have to type it again and again. A saved
search collection is created (folder with magnifying glass). This collection is automatically
updated every time you add a reference matching the query you saved.
EXERCISE Create a saved search collection and test it.
Personal notes
Create a workflow
[This is based on an idea described by Lincoln Mullen exposed in a blogpost
not availbale on the web anymore18
.]
All these management tools (tag, saved search) can help you create a simple
and powerful workflow to track what you want to read, what you already read
but was not meaningful and what you want to keep for citing.
18 http://lincolnmullen.com/archives/2009/08/how-to-create-a-work-flow-in-zotero/ [blogpost not online
anymore]
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22.
CREATE
There are several to create a bibliography.
The two easier ways are drag and drop or copy and paste references from Zotero in a word
processor.
You can create a bibliography to publish it online as well (right-click > Create
Bibliography from Selected Items... > Output Method: Save as HTML).
EXERCISE Create a bibliography (max. one page) and print it.
Personal notes
EXERCISE Create a bibliography meant to be published online and open it in your
web browser.
Personal notes
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23.
SHARE
You have three ways to share your references. Each fits different needs.
Export
You can export your entire Zotero library (Actions > Export Library...), one collection
(right-click > Export Collection...) or only a some references (right-click >
Export Selected Items...). Choose the Format in the prompt.
Sync
You can also sync your Zotero library across several devices (computers, tablets,
smartphones). It's the best way to always access your up-to-date Zotero library from anywhere
(at home, at work, even while travelling).
You need an account on zotero.org to be able to sync your data. Then just click on the Sync
with Zotero Server button (green arrow).
If it's the first time you sync your library, you need to enter your username and password
(Actions > Preferences... > Sync Tab > Settings).
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24.
You can choose to sync attachment or not (PDF, snapshots, ...). You have 300Mo free storage
space on your Zotero online account. It is enough for references only, but you may quickly
reach this limit if you store PDF files online.
You have two options: pay for more storage space19
or choose a third-party storage service to
sync PDF files (see More section).
At EPFL, I recommend you to use SWITCHdrive : http://www.switch.ch/en/drive/ (accessed
Jan. 28, 2015).
EXERCISE Go to https://www.zotero.org/user/login/ and log in to one of the
course account (you can also create a personal account here:
http://www.zotero.org/user/register) and take a tour in the settings section.
Then sync your locale Zotero library with the Zotero server.
Personal notes
Collaborate
Zotero offers a great feature for collaboration : group libraries. You can create a group, invite
members and work together on the same collection of references. When you are part of
project, you need to share with parnters. Easy with Zotero.
You add references in group (sub)collections the same way you do it in your own library.
Notice that you can grab references from a group library and pull them to your Zotero library.
EXERCISE Create a group and invite members. Add references (change Group
Settings if necessary).
Personal notes
19 https://www.zotero.org/settings/storage (accessed Jan. 28, 2015)
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25.
CITE
The main reason to collect reference is to be able to cite them when you write a paper.
Unless you use Zotero Standalone, you need a second tool to cite while you write: a plugin for
your word processor.
You can get it here: http://www.zotero.org/support/word_processor_plugin_installation
(accessed Jan. 28, 2015)
Choose the plugin depending on the operating system and word processor you are using. This
plugin is (installed as) a Firefox add-on.
When installed, the plugin appears as a Complement Tab (in Word for Windows) or a
toolbar (in OpenOffice.org/LibreOffice/NeoOffice).
LibreOffice
Word (Windows)
Word (Mac)
If you are a LaTeX user, you just need to create (export) a .bib file (Actions > Export
Library...) to be able to cite references in your paper20
.
Citation style
The way an in-text citation and/or a reference is formatted depends on the
citation style.
See this example of a book displayed in 4 different citation styles.
Chicago Manual of Style (author-date)
Puckett, Jason. 2011. Zotero : a guide for librarians, researchers, and
educators. Chicago: Association of College and Research Libraries.
IEEE
[1] J. Puckett, Zotero : a guide for librarians, researchers, and educators.
Chicago: Association of College and Research Libraries, 2011.
Nature
1. Puckett, J. Zotero : a guide for librarians, researchers, and educators.
(Association of College and Research Libraries: Chicago, 2011).
ISO-690 (auteur-date)
PUCKETT, Jason, 2011. Zotero : a guide for librarians, researchers, and
educators. Chicago : Association of College and Research Libraries.
ISBN 9780838985892 0838985890.
20 In order not to have to export your library everytime you add a reference, Robin Wilson developped a plugin
for Zotero that automatically updates the .bib file when a change occurs in your Zotero library (see More
section).
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26.
As a result, a document can look differently according to the citation style
applied. Some information is dropped in a style (e.g. ISBN) and some others
are formatted differently (e.g. author firstname). They don't always appear in
the same order.
There are two main citation style families: author-date and numeric21
. Author-
date styles format in-text citation as below and sort bibligraphy alphabetically
based on the first author lastname:
As Jason Puckett says at the beginning of his book « any book about software
inevitably starts to show its age even before it makes it to the shelf » (Puckett
2011, X).
Numeric styles insert a number in the text and sort references in the same order
in the bibliography:
As Jason Puckett says at the beginning of his book « Any book about software
inevitably starts to show its age even before it makes it to the shelf » [1].
A third citation style family exists, mostly used in social sciences and
humanities, where references are inserted in footnotes.
There are almost as many citation styles as there are scientific journals. You can choose a
style in the Preferences panel (Actions > Preferences... > Export Tab > Default
Output Format). Out of the box, Zotero provides about 15 citation styles.
For your personal styles management, go to Actions > Preferences... > Cite Tab >
Styles. If you need additional styles, click on the Get additional styles... link. This
leads you to the Zotero styles repository22
(http://www.zotero.org/styles/).
EXERCISE Install the plugin corresponding to your word processor, write
something and cite documents from your Zotero library.
Personal notes
EXERCISE Change the citation style that fit your needs.
Personal notes
21 In the Humanities field, people use a third family of styles where references are added in the footnotes.
22 This repository is also used by Mendeley, Papers and some others... See http://citationstyles.org/ for more.
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27.
MORE
If you want to go beyond the scope of the course, here are some useful tips.
Your web browser is not compatible with Zotero yet.
At the moment, only Firefox, Chrome and Safari are compatible with Zotero. The Zotero
bookmarklet allows Zotero users to use another browser (e.g. Opera).
You can get it at http://www.zotero.org/downloadbookmarklet (accessed Jan. 28, 2015)
You want to install the citation plugin but Firefox is not installed.
Citation plugins (for Word or OpenOffice.org/LibreOffice/NeoOffice) are installed in Firefox.
If Firefox is not installed on your computer, the only way to use them (without installing
Firefox) is to use Zotero Standalone (citation plugins included).
You want to sync your PDF files with a third party service.
You have 300Mo available on Zotero servers. If you want more, you can pay for that or sync
your files with a third party service. In order to be able to do that, choose a service with
WebDav protocol enabled.
At EPFL, SWITCHdrive is recommended because it offers you 25Go for free, with WebDav
enabled and is provided by an institution, SWITCH (www.switch.ch), that supports swiss
universities for years.
To use SWITCHdrive, you need to create an SWITCHcloud ID. As it is based on
SWITCHaai, this only takes a few seconds. SWITCHaai asks you to log in with your EPFL
credentials.
Then update settings in the Zotero Preference panel (Actions > Preferences... > Sync
Tab > Settings) and refresh.
You are looking for a citation style , but you don't know its name.
You may need a citation style without knowing its name, but you know what citation and
references should look like. A great tool will help find it:
http://editor.citationstyles.org/searchByExample/
You can enter a reference and it will show you matching citation styles. Easy. If you find the
right style, you can save it.
And if it's not exactly what you need, you can edit the style through the graphic interface (no
coding!) and save it: http://editor.citationstyles.org/visualEditor/.
You need a new citation style.
If you need a citation style that doesn't exist and/or that is too different from the existing
styles, you have two ways to get it.
If you XML coding skills, you can do it by yourself. All you need to know about the CSL
langage is here: https://github.com/citation-style-language/documentation.
If don't have the required skills, you can try to do it with the new graphic interface:
http://editor.citationstyles.org/visualEditor/.
But the easiest way is to ask for a new style on the Zotero forum: https://github.com/citation-
style-language/styles/wiki/Requesting-Styles
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28.
You are a LaTeX user and don't want to export the .bib file again and again in order to
have an up-to-date file to use.
A PhD student, Robin Wilson, faced the same problem, so he developped Autozotbib, a
Zotero plugin that automatically updates the .bib file when you add new things in your Zotero
library.
http://www.rtwilson.com/academic/autozotbib
You want to get PDF from references you have in your Zotero library.
This is currently not possible. This feature was requested by users and is planned. But not
very soon23
.
You need more than one Zotero library.
You are teaching as well as publishing and you don't want to mix it all up in one Zotero
library.
It is easy to have two different Zotero libraries on a computer by using both Zotero for Firefox
and Zotero Standalone, and to choose them not to share the same library.
If you need more than two Zotero libraries, it is possible to create several Zotero libraries, but
you need to create several Firefox profiles. This is an advanced feature. Each profile can
contain a different Zotero library.
To create a second Zotero library, you need to :
1. Open Firefox ProfileManager (see Swisher et Beckwith, 2012)
2. Create a new Profile
3. Install Zotero and start working
Keep in mind that the citation plugin in your word processor will be able to communicate
with only one of your Zotero library. You can encounter some troubles when trying to cite.
But it's easy to solve : you just need to reinstall the citation plugin in the Preferences panel
(Actions > Preferences... > Cite Tab > Word Processors > Reinstall...
button).
You want to have your own « Zotero server ».
For privacy concerns, you may keep your Zotero data on your own server instead of the
Zotero servers (that are in the USA). Mark Sample described a way to reproduce this
architecture with syncing and sharing functionalities (Sample, 2012).
You want to know what's happening about Zotero.
Roadmap (last updated Apr. 5, 2012): http://www.zotero.org/support/development_roadmap
(accessed Jan. 28, 2015)
23 http://forums.zotero.org/discussion/26140/get-pdf-from-references-in-library/ (accessed Jan. 28, 2015)
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